It is known from present-day climates that both temporal and spatial variations in precipitation can be more pronounced than those in temperature and thus influence ecosystems and human society in more substantial way. However, very little is known about such variations in the past. Here we present an analysis of 206 palaeoprecipitation data from two twelve million year long proxy records of precipitation for Southwest (Calatayud-Teruel basin) and Central Europe (Western and Central Paratethys), spanning the late Early and Middle to Late Miocene (17.8-5.3 Ma) at a temporal resolution of about 80 kyr and 200 kyr, respectively. The estimates of precipitation are based on the ecophysiological structure of herpetological assemblages. The results show that precipitation variations in both regions have large amplitudes during the Miocene with comparable temporal trends at longer time scales. With locally 300 mm up to more than 1000 mm more rainfall per year than present, the early Langhian and the Tortonian were relatively wet periods, whereas the late Langhian and late Serravallian were relatively dry, with up to 300 to 500 mm less precipitation than present. The most humid time intervals were the early and middle Tortonian washhouse climate periods. Overall, our data suggest that the latitudinal precipitation gradient in Europe from the Middle to Late Miocene were highly variable, with a general tendency towards a reduced gradient relative to present day values. The gradient decreases during cooling periods and increases during warming periods, similar to results from simulations of future climate change. Interestingly, the precipitation gradient was reversed during the second washhouse climate period and the Early Messinian, which may have causes a negative hydrologic balance in the Eastern Paratethys during the latter time. Yet, our reconstructed gradient curve shows no direct correlation with the global temperature signal from oxygen isotopes, which implies a non-linear regional response. Our results further suggest that major fluctuations in the precipitation gradient can be responsible for shifts in ecosystem distribution, and particularly, for faunal turnover in South Western Europe.